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  • Find Donor ID for "H0351.1015" (id = 15496)
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor,
    rma::criteria,[name$eq'H0351.1015'],
    rma::options[only$eq'donors.id']
    
  • Find Structure ID for "locus ceruleus" (id = 9148)
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure,
    rma::criteria,[name$il'locus ceruleus'],ontology[name$eq'Human Brain Atlas'],
    rma::options[only$eq'structures.id']
    
  • Find Probes associated with gene SLC6A2 (id = 1023146,1023147 )
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Probe,
    rma::criteria,[probe_type$eq'DNA'],products[abbreviation$eq'HumanMA'],gene[acronym$eq'SLC6A2'],
    rma::options[only$eq'probes.id']
    
  • Use Donor, Structure and Probe IDs as parameters to the connected service
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.json?criteria=
    service::human_microarray_expression[probes$eq1023146,1023147][donors$eq15496][structures$eq9148]
    

The output of the service is two top level ordered arrays "probes" and "samples". For example:

Code Blocknoformat
"probes":[{
    "id":1023146,
    "name":"A_23_P358345",
    "gene-id":6494,
    "gene-symbol":"SLC6A2",
    "gene-name":"solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2",
    "entrez-id":6530,"chromosome":"16","start-position":"n/a","end-position":"n/a",
    "expression_level":["13.2802","13.9603","13.9650"],
    "z-score":["9.3381","9.8663","9.8700"]},
    {
    "id":1023147,
    "name":"CUST_16472_PI416261804",
    "gene-id":6494,
    "gene-symbol":"SLC6A2",
    "gene-name":"solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2",
    "entrez-id":6530,"chromosome":"16","start-position":"n/a","end-position":"n/a",
    "expression_level":["8.1878","8.5644","8.2310"],
    "z-score":["9.3201","9.8326","9.3790"]}
    ],
"samples":[
    {"donor":{"id":15496,"name":"H0351.1015","age":"49 years","color":"C2C200"},
    "sample":
        {"well":148955246,"polygon":127107914,"mri":[95,121,126]},
        "structure":{"id":9149,"name":"locus ceruleus, Left","abbreviation":"LC","color":"00FFAA"},
        "top_level_structure":{"id":9135,"name":"Pontine Tegmentum","abbreviation":"PTg","color":"00FFAA"}},
    {"donor":{"id":15496,"name":"H0351.1015","age":"49 years","color":"C2C200"},
    "sample":
        {"well":148955204,"polygon":126786164,"mri":[97,151,131]},
        "structure":{"id":9149,"name":"locus ceruleus, Left","abbreviation":"LC","color":"00FFAA"},
        "top_level_structure":{"id":9135,"name":"Pontine Tegmentum","abbreviation":"PTg","color":"00FFAA"}},
    {"donor":{"id":15496,"name":"H0351.1015","age":"49 years","color":"C2C200"},
    "sample":
        {"well":156435966,"polygon":126789834,"mri":[96,159,134]},
        "structure":{"id":9149,"name":"locus ceruleus, Left","abbreviation":"LC","color":"00FFAA"},
        "top_level_structure":{"id":9135,"name":"Pontine Tegmentum","abbreviation":"PTg","color":"00FFAA"}}
    ]

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  • Find Structure ID for "thalamus" (id = 4392)
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure,
    rma::criteria,[name$il'thalamus'],ontology[name$eq'Human Brain Atlas'],
    rma::options[only$eq'structures.id']
    
  • Find Structure ID for "cerebral cortex" (id = 4008)
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure,
    rma::criteria,[name$il'cerebral cortex'],ontology[name$eq'Human Brain Atlas'],
    rma::options[only$eq'structures.id']
    
  • Use Structure IDs as parameters to the connected service
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=service::human_microarray_differential
    [structures1$eq4008][structures2$eq4392][sort_by$eq'fold-change']
    
  • Visualize the same search result in the Web application 

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  • Find Probe ID for probe "CUST_11451_PI416261804" (id = 1052410)
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Probe,
    rma::criteria,[name$eq'CUST_11451_PI416261804'],
    rma::options[only$eq'probes.id']
    
  • Find Structure ID for "Brain" (id = 4005)
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Structure,
    rma::criteria,[name$il'brain'],ontology[name$eq'Human Brain Atlas'],
    rma::options[only$eq'structures.id']
    
  • Use Probe and Structure IDs as parameters to the connected service
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=service::human_microarray_correlation
    [probes$eq1052410][structures$eq4005]
    
  • Visualize the same search result in the Web application

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  • Download links for all MR and DTI data available
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor,
    rma::criteria,products[abbreviation$in'HumanMA','HumanSZ','HumanCtx','HumanSubctx'],organism[name$il'Homo Sapiens'],
    rma::include,specimens(well_known_files(well_known_file_type[name$in'T1-MRI','T2-MRI','DTI-MRI'])),
    rma::options[only$eq'donors.name,products.name,well_known_files.download_link,specimens.id']
    
  • Download TI MR scan for donor 'H0351.2002'
    Code Blocknoformat
    http://human.brain-map.org/api/v2/well_known_file_download/157723301
    
  • Download the MR to MNI transform parameters
    Code Blocknoformat
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::Donor,
    rma::criteria,products[abbreviation$eq'HumanMA'],
    rma::include,specimens[parent_id$eqnull](alignment3d),
    rma::options[only$eq'donors.id,donors.name,specimens.id']
    

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